Memories and Secrets
by lemonsherbertshadowhunter
Summary: This is a story of snippets on what Clary would have been like if she grew up with Johnathan. Watch how Clary trains with her brother and her friend Jace that lives with them. What will CLary do when something terrible happens to her family and she is snatched away by hooded figure? Rated T just in case.
1. Prologue

DISCLAIMER: I don't own anything. For I am not Cassandra Clare.

Secrets: Prologue

Johnathan's point of view.

I sat in my room wondering what took father so long tonight. He said he was going out and would be back before dinner. Normally I wouldn't care but this time he said he was going to bring back a surprise for me. I am brought back out of my thoughts by heavy footsteps _'Father'_ I think to myself. I heard the door to the bedroom next to mine shut. I quietly snuck out of my room and opened the door gently. What I saw next surprised me. It was the image of my father standing beside a white crib. From where I stood I couldn't see what was in the small white crib. I shut the wooden door with a bang my father jumped in surprise " Johnathan,son come here for a minute, I'd like you to see your surprise." I slowly made my way down the room. I looked into the crib and saw a tiny little baby girl in a nice green silk dress. She was staring into my eyes which were pitch black unlike hers which were a beautiful emerald green. She started giggling and I just looked over to my father. "Johnathan, meet your little sister Clarissa." The little girl looked over to her father when her name was mentioned. She looked nice enough with green eyes and curly red hair. 'you know, I actually think I'll like her.' I thought to myself. I picked her up and hugged her to me. " Hey there little sister." I said with a small smile on my face.

*####*

A/N: okay I know that was short but that's only the prologue. The next chapters will be longer I promise. They are just gonna be loads of paragraphs of when Clary is growing up. Oh and just so you know this is my first fan fiction and my first real story altogether not counting the ones from school of course. So I guess I'll see you on the next chapter guys.  
So review if you would like next chapter will be up in a while. Criticism is welcome and so are ideas. :D


	2. Chapter 1 Memories

Secrets: Chapter One: Memories

Third-person view

"Will you stop it Johnathan!" Clarissa Morgenstern hissed at her older brother. " Only if you say the magic word little sister." he replied throwing another knife at the library wall. " Johnathan,may you please stop throwing your knives at the wall because I am unable to concentrate in my book." the younger sibling asked. Clarissa was five years old now and her brother Johnathan was six,even though he looked ten." All you had to do was ask politely. What'cha readin' there sis. No wait today is Tuesday which means you are learning Latin. Am I correct?" "Yes" "Yes am always correct. I can't wait until you get your first mark cause then we'll be able to train together, cause I know how boring it is to be learning languages all day every day." "Well you only have to wait until tomorrow." *#####*

**Tomorrow**

" Sit down Clarissa." Valentine said. His daughter did as she was told. ' It's only going to sting a bit Clarissa.' Brother Enoch said or rather thought. "Father don't you think Clarissa is a bit too young, she's only five." Johnathan Morgenstern whispered to his tall father. "No. Clarissa is strong. She is not too young." their gather replied quickly yet smoothly." If you say so, father." The Silent Brother got out his stele and took Clarissa's right hand in his he placed the tip of the stele onto her hand. It stung a little but it wasn't sore. Once Brother Enoch was finished Clarissa stood up and went over to her father. " I dud it daddy,look isn't it just beautiful?" she twirled lightly in her white dress. " I is sweetie, now its time to open your presents." "Ooohh presents!" "This one is from me ." said her brother giving her a long narrow case. She opened it and saw a beautiful silver stele. " Really?! Thank you so much big brother." Clarissa replied and hugged him. Lots of her other gifts were gifts a shadowhunter would receive such as a witchlight stone,gear,seraf blades and books. Many of the other gifts were clothes, paints, books,ect. " At least now I'll have a training partner." *#####* "Don't you wanna practise Clary?" Johnathan asked his sister Clarissa who was sitting in a nearby tree while her brother practiced his knife skills. Johnathan started to call his sister 'Clary' because 'Clarissa' was too long."No, because father doesn't give us free days often but when he does, I like to relax. Maybe I should go see the Lightwoods? What do you think?" " Sure,why not." her brother replied." As long as you tell father first." "Alright," Clary sighed. "see you in a while." "Bye." *######*

Clary knocked on the Lightwoods door. A moment later a tall, young girl opened the the door. "Oh, hey Clary. How are you? Come in,come in." Isabelle opened the door wider. " Hi Izzy." Clary said as she stepped inside. "What brings you here?" Isabelle asked as she closed the door. " Oh, nothing really. Just thought we could hangout, you know." "Sure, let me just go and change and get Alec." Clary followed her friend upstairs to her room. Clary spent the next half hour watching her friend get dressed. "Come on Izzy,you look fine." "Are you sure?" "Yes! Now, come on!" " Okay,okay. Alec! I'm going out with Clary!" "Did your brother here that?" " I don't know, but who cares?" Clary just shook her head. *#####* Clary was outside her fathers study. She was listening in on a conversation between her father and Johnathan. She knew it was wrong to eassedrop, but being a nine year old child, curiouscity got the better of her. She couldn't make out much but she did get a few words like Herondale boy, Wayland Manor,gold hair,gold eyes,staying here and be nice. Clary tried to put it together she understood most of it. That evening Clary went to see the Lightwoods. She asked Isabelle if she knows who lives in the Wayland Manor and it turns out she doesn't and Clary explains about the conversation her father and brother had. " Well maybe he's a family friend and he's coming to stay for a while?" " I don't know. Look I'll probably see you tomorrow, or something." "Bye."

*######* *Next Week*

Clary woke to a pounding on her door. She sat up and swung her legs over the bed. She stood up and walked over to her door and opened it. In the doorway stood her brother his hand in the air ready to knock on her door again. " What? " Clary asked groggily. She knew it was really early because if she woke up at her usual time she wouldn't be sleepy. " Father wants to see us in his study now. Don't bother getting dressed okay?" Clary swallowed hard. Her father never lets them into his study. She has only been there once and that was when he explained about how their blood was tainted with demon and angel blood. (A/N I'm sure you can figure out who's blood is tainted with what) Clary stepped out of her room and shit the door. " Do you know what he wants?" Clary asked. " I think I do." " Well, why don't you share your thoughts with me big brother." " Cute. But no. Sorry little sister." " You know how to play a though game, Johnathan." "Of coarse I do." They had reached their fathers study. Johnathan knocked on the door three times. There fathers coarse voice said "Come in." And so they did. "Clarissa, Johnathan. I have someone I'd like you to meet."


	3. The Blond Rat

**Disclaimer**: I do not own The Mortal Instruments. I wish I could though, it'd be fun.

Any way hope you enjoyed the last chapter. I promise the chapters will get longer.

**Chapter 2**: _The Blonde_ _Rat_.

Clary sat opposite her father at the large oak table.  
" _Jonathan_ come here." Valentine said. Clary looked over to her brother but he didn't move. Then the door at the back of the study opened and out came a boy who looked no older than Clary. He had bright blonde hair and hold eyes. His skin was a nice gold colour aswell. He looked like a god, and Clary hated him. She threw him a glare she looked taken aback for a second. " Clarissa, Johnathan this is _Jonathan_ Wayland. He shall be staying here for a while." Valentine said. His voice hard. " Clary be nice and show a room next to yours."  
Clary scowled. " Of course father."she muttered. She turned to go out the door and turned around. " are you coming or not?" she asked angrily and sauntered out the room. _Jonathan_ looked over to valentine " Did I do something wrong?" he asked  
" No" Valentine _replied._  
_Jonathan_ had to jog to catch up with Clary. For a small girl she has a fast pace. _Johnathan_ thought to himself. They went down a few longer corridors until Clary stopped. _Johnathan_ would've fell on top of her if not for his brilliant shadowhunter skills. Clary stood in the middle of the corridor. She pointed to a door on the left. " That's your room," she then moved her hand to the other side of the hall and pointed to a " that's my brothers and that's mine." she continued. " Now if you don't mind im going to go change."

Anyway I know that was really short but im starting school tomorrow and well I've been busy. Oh and before i forget i want to ask my lovely friends would you like shorter chappies and updates often or longer chappies but less frequent updates? It would really help. Well I'll talk to you in the next chapter see ya!


	4. Chapter 3 My Morning Encounter

**Disclaimer:**_** I do not own The Mortal Instruments and I don't plan on owning them anytime soon.**_

Chapter 3: Morning Encounter With Goldilocks.

(Clary)

I was woken once again to a knock on my door. I rolled out of bed and stood up I checked my alarm and it read 5.30 am. ' Five-thirty! Who in their right mind would wake up and this unearthly hour especially on a Sunday.' I thought to myself. I yanked the door open and was greeted by the sight of Jace leaning against the doorframe. I stared up at him with a glare. "What do _you _want?!" asked him quite sharply. "Well I woke up and was hungry so….," he drawled on " I thought you could show me to the dining room or even the kitchen?" he ended the sentence as a question." First, we're not allowed in the kitchen and second, we _all _sleep _in_ on _Sundays_, so breakfast won't be served till ten. Now please go away. I answered harshly adding extra harshness to the Sunday bit. "Well can you show me to the training room?" he went on. I groaned " Figure it out yourself." I said and shut the door on him. I drew a locking and soundproof runes on it and climbed into bed.

When I woke up again it was 9:00 am. _Perfect. _I thought. An hour and a half off training outside and then half an hour to get ready. I jumped out off my bed and tugged on some dark jeans, a green halter top and my favourite black combat boots. I climbed out the window and closed it behind me. I hopped onto the old oak tree that was beside my window. This self-morning training usually consisted of me jumping from branch to branch of nearby trees. It helped clear my mind and it sharpened my agility. As I came to a stop back at the old oak tree I was dripping in sweat. I slid the window open and walked into the shower. I stipped off all my clothes and went into the shower.(A/N I changed Clary's age to 7 instead of nine okay.) I'm pretty sophisticated for a seven year old,I mean I know what I have to do, when to do it, how to do it and where to do it. As I stepped out of the shower I pulled a towel on me and let my hair loose. I turned the tap on and brushed my teeth. In the middle of this process I heard someone walking in my room. 'Just Johnathan I guess.' I thought to myself. I turned off the tap and went out the door. I stepped into the room and saw jace once again. This time though he was sitting on my bed flicking through one of my many sketchbooks. Now I really hate you. I raised one my dark eyebrows and coughed.

His eyes darted up and when he saw me in only a towel he flushed red. "I-I-I was just g-going to ask you-" he didn't get to finish because I interrupted him " What in the name of the Angel what do you think you are doing in here?!" I asked him loudly. But oh I wasn't finished yet. " How dare you come in here without asking and how dare you invade my privacy by looking through my personal things?! Out," I ordered him. He didn't move. " I said out!" he looked scared and hurt flashed across his amber eyes but it disappeared almost instantly.

**Okay I know it's short and it"s been over a month but you would have reviewed it might have been done faster and longer. So I'll ask again please review and I'll see you later, and if you want to see Clary's outfit I have it on my page. Bye :)**


	5. Chapter 4

**_Disclaimer: I unfortunately do not own TMI nor will I ever *cue the tears*_**

**_Anyway this just a short author note saying " OMG OMG three reviews YAY YAY!_**

**_tmilover122: thank you for the suggestion it helps. ;D_**

**_greygirl2358: all shall be answered soon enough and as a spoiler she does snap out of it. Once I do a few evil things. *laughs evilly* And I changed her age because if say I plan her to stay three years in Idris she'll be ten the same age Jace was when he went to the institute. But she was nine now and spent three years in Idris it wouldn't _**  
**_fit in with the time frame, if you get me. Don't worry if you don't 'cause sometimes even I don't understand myself._**

**_Fishpuppy: I hope you get better soon!_**

**_Chapter 4: Shopping With Izzy._**

**(Cary)**

I felt slightly guilty after I shouted at Jace but oh well he deserved it. I took my sketchpad and placed it beside my bed. i turned and headed towards my wardrobe to get my outfit. I chose a nice red top, these lovely forest green/turquoise pants and black toe pumps with a black bow on them. I brushed my hair and tie it up in a ponytail. As I headed to the door I checked my watch. 10.55, yikes! I ran down the corridors, which thankfully were deserted of maids, reached the dining room just in time. I stopped and regained my breath. I pushed open the door and you won't be able to guess what I saw. Com'mon I'll give you a second….. okay you still don't know well, I'll explain. Since my father sits at the head of the table my brother obviously sits on the right so that leaves me sitting on the left of Valentine. But today father's seat was empty and Johnathan was in his seat buttering a slice of toast, and across from him, in my seat was Jace. He hasn't yet noticed me and was inspecting the plate for some reason. I once again cleared my throat. Jonathan looked up and smiled then looked to Jace "You might want to get out of that seat if you wanna live to see double-digits," Jace just looked up at me and raised one of his blonde eyebrows. "Yes….?" he drawled on.  
"You're sitting in my seat." I said as sweetly as I could.  
"I am? I haven't noticed."he answered with a smirk  
"Well, would you please move?" i asked.  
" Make me." and that's all it took. What I did next was not something you would expect from a sweet seven year old, but you see I'm not that sweet when blondes tick me off. I lunged at him, right across the table and knocked him off his chair. He fell backwards and I fell on top of him we rolled around the floor shouting insults at each other and throwing in a few punches here and there, all while Jonathan ate his god-damned toast.I was on top of Jace when we heard the door to the room open and close, we froze but then continued rolling on top of each other. "What is going on here?" I heard my father say.  
" Oh you know, the usual sibling banter they have I think it's their third one today. This time Jace sat in Clary's seat so she asked him to get out of her seat. Politely, if I may add. And then Jace said 'Make me'. so she did." The next thing I notice is that I'm being lifted off Jace but no matter what i still keep flailing my arms around madly. " Stop it, Clarissa.'' I did and was left hanging there in my father's hands, while Jace sat on the floor. "Now I don't want to see you two even look at each other during breakfast. Understood?" Valentine said. " Yes father.' both of us mumbled. I shot him a glare. My father let go of me and I dashed towards my seat and unfortunately Jace chose to sit right beside me. I tried to ignore him but it was kinda hard when he kept nudging me with his legs and throwing bits of bread at me. The table was quiet so I decided to start up a conversation "Did you know that dime has 118 ridges and a quarter has 119?" The question was aimed to Jonathan but if course Jace just had to answer. " How do you know that? Were you that bored that you actually counted?" he said smirking. Who knew an eight year old could be so evil. I pushed my plate away from me and stood up," if you excuse me, I am no longer hungry." I say and walk out of the room. I strut up the two flights of stairs to get to the third floor corridors. I walk silently to my bedroom and close it tightly. I change into my gear and head to my desk. I open the middle drawer and take out three daggers, strap them to my my belt and grab my stele before locking the drawer with a key. I step over all the clothes on the floor and walk towards the window the second time today. ''I really should clean this place up,'' I say to myself. The floor was littered with expensive clothes from all over the world, the wall was nearly fully painted and the desk was overcrowded with papers of all colours. They were quotes that I was collecting. Things like, 'If opportunity doesn't knock,build a door.', 'You only live once but if you do it right, once is enough.' and of course my personal favorite ' A mother's love is patient and forgiving when all others are forsaking, it never fails or falters, even though the heart is breaking.' I hated that one, it wasn't true, at least not to her. I jumped out the window not even bothering to land on the tree, and ran full sprint through the forest in the Lightwood's house direction. I had gotten a letter yesterday from Isabelle saying she was in Idris for a while. Usually whenever she was here it meant that we would have to go shopping in Alicante for new  
clothes, weapons, etc. I got to their front steps quite quickly. I wasn't breathing too heavily so I wouldn't have to explain why I ran here. I knocked on their brown door three times like I always do and waited 25 seconds like I always do. This time Isabelle's mom answered the door. She was tall and willowy like Isabelle and had the same jet black hair, though her eyes were blue unlike her daughter's brown ones.  
''Hello Clary, how did you know we were here?'' she asked me pleasantly.  
''Hi . Isabelle sent me a fire message. Is she here right now?'' I asked her.  
''Yes, I'll go get her now.''  
I waited by the door for a minute until Alec walked by.  
'' Hey Clary what are you doing here?'' he asked me curiously  
''Oh, you know waiting for your sister. The usual,'' I giggled. You could say I had a teenie tiny crush on him. Alec of course, was oblivious to it.  
''Well then, I have to go, see you.''  
Just then Izzy came stumbling down the stairs. She ran right up to me and launched herself at me. If it wasn't for my shadowhunter training, I would've fallen on my backwards. Izzy as always was wearing a skirt. This one was short and yellow. It was accompanied with a white sleeveless blouse and dark chocolate coloured sandals. She looked gorgeous, like always.  
'' Hey!'' she squealed  
''Hi, you wanna go to Alicante?'' I asked her meekly. ''I have some stuff to tell you about.''  
''Okay!'' she answers cheerfully. And we walk off in the direction of Alicante.


End file.
